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A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology
(Public Library of Science, 2017)
[Abstract]
Background:
We consider a general class of global optimization problems dealing with nonlinear dynamic models. Although this class is relevant to many areas of science and engineering, here we are interested ...
MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud
(Oxford University Press, 2017)
[Abstract] This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted ...
ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models
(Oxford University Press, 2019-08-21)
[Abstract] ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two ...
High performance genetic algorithm for land use planning
(Pergamon Press, 2013)
[Abstract] This study uses genetic algorithms to formulate and develop land use plans. The restrictions to be imposed and the variables to be optimized are selected based on current local and national legal rules and ...
Enhanced global optimization methods applied to complex fisheries stock assessment models
(Elsevier BV, 2019-04)
[Abstract]
Statistical fisheries models are frequently used by researchers and agencies to understand the behavior of marine ecosystems or to estimate the maximum acceptable catch of different species of commercial interest. ...
Assessing resilient versus stop-and-restart fault-tolerant solutions in MPI applications
(Springer New York LLC, 2017-01)
[Abstract] The Message Passing Interface (MPI) standard is the most popular parallel programming model for distributed systems. However, it lacks fault-tolerance support and, traditionally, failures are addressed with ...
Enhanced parallel Differential Evolution algorithm for problems in computational systems biology
(Elsevier BV, 2015)
[Abstract] Many key problems in computational systems biology and bioinformatics can be formulated and solved using a global optimization framework. The complexity of the underlying mathematical models require the use of ...
Novel parallelization of simulated annealing and Hooke & Jeeves search algorithms for multicore systems with application to complex fisheries stock assessment models
(Elsevier Ltd, 2016-11)
[Abstract] Estimating parameters of a statistical fisheries assessment model typically involves a comparison of disparate datasets to a forward simulation model through a likelihood function. In all but trivial cases the ...
BPLG–BMCS: GPU-sorting algorithm using a tuning skeleton library
(Springer New York LLC, 2017)
[Abstract] In this work, we present an efficient and portable sorting operator for GPUs. Specifically, we propose an algorithmic variant of the bitonic merge sort which reduces the number of processing stages and internal ...
Facilitating the development of stencil applications using the Heterogeneous Programming Library
(2017)
[Abstract] Stencil computations are very common in scientific codes. Heterogeneous systems achieve good results solving these problems, but their programming is complex because of the ghost regions required in multi-device ...